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BULLKpy 0.1.0 documentation

  • Installation
  • API reference
  • Notebooks
  • GitHub
  • Installation
  • API reference
  • Notebooks
  • GitHub

Section Navigation

  • bullkpy
  • Input Output
    • Read counts
    • Add metadata
  • Pre-processing
    • Batch correction with Combat
    • Filter genes
    • Filter samples
    • Find bad Obs columns
    • Highly variable genes
    • log1p
    • Make Obs .h5ad safe
    • Normalize cpm
    • QC metrics
    • Sanitize metadata
    • Set raw counts
    • Is integerish
  • Tools
    • Adjusted rand index
    • Association
    • Categorical association
    • Clustering
    • Cluster metrics
    • Differential expression
    • Negative binomial GLM differential expression
    • Gene-Category association
    • Gene-gene correlations
    • GSEA preranked
    • Leiden resolution scan
    • List enrichr libraries
    • Neighbors
    • Obs-Category association
    • Obs-Obs correlation matrix
    • Pairwise posthoc
    • Partial correlations
    • Principal Component Analysis
    • PCA loadings
    • Plot Correlation heatmap
    • Plot Correlation scatter
    • Posthoc per gene
    • Rank genes categorical
    • Rank genes groups
    • Score genes
    • Score cell cycle genes
    • Score genes from a dictionary of genes
    • Top gene-gene correlations
    • Top Gene-Obs correlations
    • Top Obs-Obs correlations
    • UMAP embedding
    • UMAP graph
  • Plotting
    • ARI resolution heatmap
    • Association heatmap
    • Boxplot with statistics
    • Categorical confusion
    • Correlation heatmap
    • Correlation plot
    • Dotplot
    • Dotplot association
    • Gene Association
    • Gene Association Volcano
    • Gene Plot
    • Genes vs. mitochondrial fraction
    • GSEA bubbleplot
    • GSEA Leading edge heatmap
    • Heatmap association
    • Heatmap Differential Expression
    • Leading edge Jaccard heatmap
    • Leading edge overlap matrix
    • Library size versus genes
    • MA plot
    • Mitochondrial fraction vs. counts
    • oncoprint
    • PCA loadings bar plot
    • PCA loadings heatmap
    • PCA scatter plot
    • PCA variance ratio
    • QC by group
    • QC metrics
    • QC pairplot
    • QC scatter panel
    • Rankplot
    • Rankplot association
    • Rank genes groups
    • Rank genes groups dotplot
    • Sample distances
    • UMAP plots
    • Violin plots
    • Volcano plot
    • Volcano for categorial comparisons
  • API reference
  • Pre-processing

Pre-processing#

  • Batch correction with Combat
  • Filter genes
  • Filter samples
  • Find bad Obs columns
  • Highly variable genes
  • log1p
  • Make Obs .h5ad safe
  • Normalize cpm
  • QC metrics
  • Sanitize metadata
  • Set raw counts
  • Is integerish

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Batch correction with Combat

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